改进后的大鼠参考基因组提高了对实验室大鼠遗传多样性的发现。

IF 11.1 Q1 CELL BIOLOGY Cell genomics Pub Date : 2024-04-10 Epub Date: 2024-03-26 DOI:10.1016/j.xgen.2024.100527
Tristan V de Jong, Yanchao Pan, Pasi Rastas, Daniel Munro, Monika Tutaj, Huda Akil, Chris Benner, Denghui Chen, Apurva S Chitre, William Chow, Vincenza Colonna, Clifton L Dalgard, Wendy M Demos, Peter A Doris, Erik Garrison, Aron M Geurts, Hakan M Gunturkun, Victor Guryev, Thibaut Hourlier, Kerstin Howe, Jun Huang, Ted Kalbfleisch, Panjun Kim, Ling Li, Spencer Mahaffey, Fergal J Martin, Pejman Mohammadi, Ayse Bilge Ozel, Oksana Polesskaya, Michal Pravenec, Pjotr Prins, Jonathan Sebat, Jennifer R Smith, Leah C Solberg Woods, Boris Tabakoff, Alan Tracey, Marcela Uliano-Silva, Flavia Villani, Hongyang Wang, Burt M Sharp, Francesca Telese, Zhihua Jiang, Laura Saba, Xusheng Wang, Terence D Murphy, Abraham A Palmer, Anne E Kwitek, Melinda R Dwinell, Robert W Williams, Jun Z Li, Hao Chen
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引用次数: 0

摘要

第七次迭代的诺瓦格犬参考基因组组装--mRatBN7.2--纠正了大量错位的片段,与上一次相比,碱基水平错误减少了约 9 倍,连续性增加了 290 倍。基因注释现在更加完整,提高了基因组、转录组和蛋白质组数据集的映射精度。我们利用 mRatBN7.2 联合分析了代表 120 个实验鼠品系和亚品系的 163 个短线程全基因组测序数据集。我们定义了 2,000 万个序列变异,其中 18,700 个序列变异可能会影响 6,677 个基因的功能。我们还从 1,893 只异质种鼠中生成了新的大鼠基因图谱,并注释了转录起始位点和替代多腺苷酸化位点。mRatBN7.2 汇编以及对大鼠品系间基因组变异的广泛分析,增强了我们对大鼠基因组的了解,为研究人员进行大鼠研究提供了更多的资源。
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A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

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